GgaINT0024832 @ galGal4
Intron Retention
Gene
ENSGALG00000003580 | MMP2
Description
72 kDa type IV collagenase [Source:UniProtKB/Swiss-Prot;Acc:Q90611]
Coordinates
chr11:3209085-3211018:-
Coord C1 exon
chr11:3210890-3211018
Coord A exon
chr11:3209259-3210889
Coord C2 exon
chr11:3209085-3209258
Length
1631 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCA
5' ss Score
7.87
3' ss Seq
TGCATCTGTTCTCTTTGCAGTGG
3' ss Score
10.25
Exon sequences
Seq C1 exon
AACATGGTGATGGCTATCCATTTGATGGCAAAGATGGTCTCCTGGCTCACGCCTTTGCACCGGGGCCAGGAATTGGAGGAGACTCCCATTTTGATGATGATGAACTGTGGACTCTTGGAGAAGGGCAAG
Seq A exon
GTACCAAATGTTTTAATATTTCAGAACATATGGTCTGCTAACTGCTTCAGGATGTTGCTTCAGGAACTGTTTTCATTGACATGTCAATAAGTTTTAGGGGTAAATATTACTACAGATGAAAATAAGTGCATACAATTTAAATCGTTCTCAACAAAATGTTTAAGTAATTCCTAAATGTTTTGTAGAATTTCCATTCCTGTTCCTCTACCATTACTCCTTGAAAAACTGAACTGATAATAGGCCTGATGCCTCACAGCCTTGCTGAAGGGTGGGAAAAGTACAAAGCCATGACTGATTTTGAATGCTTCAGTTCTCAGGTGCCCAAGATGCAATATCACTATTAAGAGGCAAAGTGTTGGGTGCTTTTCTACTGGCACTCTCTTTTAACAGGACCTAAGCTATGATTCCAGTCTTTAAAAATTGAATCATCCACCTGAATAAGAATTTATGTACTGGTATTCATGGTATCTGTCAAAGACAAATGAAACATAAACCCCTTGTGCATAGTGGGTTAAGACCAACTTCAAGAATCTTTAGTAGGCAGTAATCTTTATAAGGAAGCAACCAAAGAGACTGTTGTGACCTTAGACAAGTATGACCAAGCAATAGTAGTGTGGAACATGTTTTATCTGCTTAAGCTTCAACACAATCATATATTGCTAACTATAATTCTTTCACTGTAAAATAAATTGGAAAACTAGGAGTAAGAATACAAACTCATGTTAGCTTTTCAGTTCAAAATGTAGTTCTCTCAGCTGTCCTCTCACTCAAAGGAAATAATTGAACTTCAATATCCAAATAGCCAAAACCCTTCTCTTTGGCTTTATTTTATCTCTAGCACAAGCACTGACGGGTAGCTGTAACTGGTAAGCATCCTTGCCTCAGAGCATGTCACGAAGTTATCTAGATCAATCTAGAAAAATCTATGCCCATGACACAAGGCAGTGGGTAAAATTACAAAACCATGACAGAGCAACAACAGTGAACAGGAGGAAACTGTTTTCCATATGTGTAGATATCCTACACAAGTATCCAATTAGTCACTGCAATTAAAAGAAATACTAAGGATATGCAAGTTGCTTGTACAGAAACATGTCTCAGAGCACCAGTAAACTTAGGAGAAGTGTTTACGTGTAACAAATAGAAATAAAGCCCAGGATCTGTGTGTGCCTGCATTACCACCAAATTGCTCGGTGCAGCAACAGATCTCATTCAAGTCAAATTGCAAATACCAAAGTCATTTATGAGGCATGAGGTATGTTGAATCTCATGCTCAACATGAACATGCTGCCTGGAAACTTTCAAAATATACTGAATATTTTAGACCACATTACCAAAGAAACTAAATTACTAAACATATTAACAGCATGTATATAAGTTTGCATTGCCAAAGTAACAACAACACATTTATTTTTCTGGGCTGATTTTAAGGACTGTTCATTCTAAGACTTCACCATGAGTAATATCTATGTAATTCTTTCAGAATTACCAGTTATTACTTCAACTATGATCACCTTGCCAATAGAGAGACCAACAACATACAGAATGTCAAAGCAGAAATCCACACTACATTTGCACCAATATCCTCCAGTCAGTGACTCATTTCAGCACTGCATCTGTTCTCTTTGCAG
Seq C2 exon
TGGTTAGAGTAAAGTATGGAAATGCAGATGGTGAATACTGCAAATTTCCCTTCTGGTTCAATGGTAAGGAATACAACAGCTGCACAGATGCAGGACGTAATGATGGATTCCTCTGGTGTTCCACAACCAAAGACTTTGATGCAGATGGCAAATATGGCTTTTGTCCCCATGAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003580:ENSGALT00000005666:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0041319=Peptidase_M10=FE(13.1=100)
A:
NA
C2:
PF0041319=Peptidase_M10=FE(17.6=100),PF0004014=fn2=WD(100=71.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTGATGGCAAAGATGGTCTCCT
R:
TGGGGACAAAAGCCATATTTGC
Band lengths:
278-1909
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]